Discrimination of human papillomavirus genotypes using innovative technique nested-high resolution melting

The prompt detection of human papillomavirus and discrimination of its genotypes by combining conventional methods in new molecular laboratories is essential to achieve the global call of eliminating cervical cancer. After predicting the melting temperature of an approximately 221 bp region of the L1 gene from different HPV genotypes by bioinformatics software, an innovative technique based on the nested- high resolution melting was designed with three approaches and using conventional PCR, qPCR, and diagnostic standards. HPV-positive samples identified by microarray along with diagnostic standards were evaluated by qPCR-HRM and discordant results were subjected to sequencing and analyzed in silico using reference types. In addition to screening for human papillomavirus, nested-qPCR-HRM is one of the modified HRM techniques which can discriminate some genotypes, including 6, 16, 18, 52, 59, 68 and 89. Despite the differences in diagnostic capabilities among HRM, microarray and sequencing, a number of similarities between HRM, and sequencing were diagnostically identified as the gold standard method. However, the bioinformatics analysis and melting temperature studies of the selected region in different HPV genotypes showed that it could be predicted. With numerous HPV genotypes and significant genetic diversity among them, determining the virus genotype is important. Therefore, our goal in this design was to use the specific molecular techniques with several specific primers to increase sensitivity and specificity for discriminating a wide range of HPV genotypes. This approach led to new findings to evaluate the ability of different approaches and procedures in accordance with bioinformatics.

Evaluation of Drug Resistant Genotypes to Fansidar and Chloroquine by Studying Mutation in Pfdhfr and Pfmdr1 Genes in Plasmodium falciparum Isolates from Laghman Province, Afghanistan

Background:

Malaria is one of the major health problems in endemic countries like Afghanistan. Evidence has been reported about reducing the effects of chloroquine against Plasmodium falciparum in many endemic countries. The aim of this study was to investigate the resistance mutations in pfmdr1 and pfdhfr genes of P. falciparum samples detected in blood samples of malaria patients in Laghman Province, Afghanistan.

Methods:

Samples were taken on DNA retention cards and 3 glass slides (thin and thick spread) from Laghman Province, Afghanistan in 2018. The pfmdr and pfdhfr mutations in 30 P. falciparum positive samples were examined using PCR-RFLP techniques. The PCR product was then sequenced to determine the mutation at the N86Y and D1246Y mutations of the pfmdr1 and N51, C59, I164, S108 and A16 points of pfdhfr genes.

Results:

In the pfmdr1 gene, all samples were wild-type and no mutation was detected at point 86 and D1246Y. In the pfdhfr gene sequences using CLC main workbench software no mutations were detected at codons 16, 51. However, some mutation was observed at codons 59, 108 and 164. These mutations were L164I, S108N and C59R.

Conclusion:

Our findings provide evidence of the possible emergence of fansidar-resistant specimens in Laghman. The data of this study provide the basis for future prospective studies in other endemic areas of Afghanistan. The absence of significant mutations in P. falciparum samples of Laghman Province may indicate that this parasite may have switched to chloroquine re-sensitization in this area.

Prevalence and determinants of self-medication with antibiotics among general population in Afghanistan

Objective: Self-medication with antibiotics (SMA) is a common cause of antibiotic resistance, a major public health problem. This research aimed to identify the prevalence of SMA and explore reasons for practicing SMA among people living in Kabul, Afghanistan.Methods: A community-based cross-sectional study was conducted from May to November 2017 in 12 community pharmacies operating across Kabul, Afghanistan. Multivariable logistic regression was conducted to identify the factors associated with the use of SMA.Results: Out of 385 participants, 282 (73.2%) practiced SMA during the last year. Overall, 241 (62.6%) were 'very concerned' about the use of SMA, and 156 (40.5%) highlighted it is bad to practice SMA. The top three antibiotics used for self-medication were penicillin (ATC class: J01C), metronidazole (ATC: P01AB01), and ceftriaxone (ATC: J01DD04). Economic problems, lack of time to visit doctors, and ease of use were cited as the main reasons for practicing SMA. Furthermore, female participants were less likely to practice SMA compared to male counterparts.Conclusion: While efforts should be directed to enforce strict drug regulations system and awareness programs, priority should be given to provide accessible, affordable, and quality health care services to increase citizen's compliance to appropriate drug prescriptions.

HLA, Immune Response, and Susceptibility to COVID-19

The severe acute respiratory syndrome caused by Coronavirus 2 (SARS-CoV-2) that appeared in December 2019 has precipitated the global pandemic Coronavirus Disease 2019 (COVID-19). However, in many parts of Africa fewer than expected cases of COVID-19, with lower rates of mortality, have been reported. Individual human leukocyte antigen (HLA) alleles can affect both the susceptibility and the severity of viral infections. In the case of COVID-19 such an analysis may contribute to identifying individuals at higher risk of the disease and the epidemiological level to understanding the differences between countries in the epidemic patterns. It is also recognized that first antigen exposure influences the consequence of subsequent exposure. We thus propose a theory incorporating HLA antigens, the "original antigenic sin (OAS)" effect, and presentation of viral peptides which could explain with differential susceptibility or resistance to SARS-CoV-2 infections.

The Comparison of Real-time-PCR-HRM and Microscopy Methods for Detection of Mixed Plasmodium spp. Infections in Laghman Province, Afghanistan

BACKGROUND

Laghman province, in the east of Afghanistan, is one of the most malaria endemic regions with prominence of Plasmodium vivax and Plasmodium falciparum. So far, no study has been conducted to investigate the extent of mixed infections in this area.

OBJECTIVE

In this study, we aimed to evaluate the prevalence of mixed infections of malaria in Laghman province by using a new and highly sensitive molecular method (real-time polymerase chain reaction high resolution melting analysis) and compare its results with microscopically confirmed cases of malaria.

METHODS

In general, 347 infected individuals have been referred to Khalwati laboratory that is located in the center of Laghman province from May to November of 2018. Microscopic analysis was performed on prepared thick and thin blood films under ×100 lens with oil immersion. The real- time-PCR-HRM assay was performed using an ABI 7500 Fast Real-time PCR system.

RESULTS

In a microscopic examination, out of 347 patients referred to the Center, 267 (76.94%) cases were detected to be Plasmodium vivax, 79 (22.76%) Plasmodium falciparum and 1 (0.28%) case of mixed of two species. However, by using Real-time PCR-HRM technique, 249 (71.75%) were detected Plasmodium vivax, 79 (22.76%) were Plasmodium falciparum and 19 (5.47%) were mixed of two species.

CONCLUSION

Our result indicated that the Real-time PCR-HRM method is more accurate and more reliable than microscopic method in the diagnosis of malaria mixed infections.

The Immune Response and Effectiveness of COVID-19 Therapies

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly pathogenic with relatively high mortality and morbidity. In addition to pneumonia, acute respiratory distress syndrome, and microembolic disorder, a high proportion of patients with SARS-CoV-2 develop lymphopenia and cytokine storm disorder. This review explores the underlying mechanisms behind the pathogenesis of SARS-CoV-2, especially the immune mechanisms, which could be potentially used as therapeutic targets for the management of COVID-19.

Application of High-Resolution Melting (HRM) Technique towards the Detection of Asymptomatic Malaria in a Malaria Endemic Area of Southeastern Iran under Elimination Program

Background:

Asymptomatic malaria, which usually exists in low parasitemia, acts as the Plasmodium species reservoirs contributing towards malaria transmission. This situation hinders malaria elimination programs in endemic areas, thus necessitating an active case detection with a high sensitive method and treatment of cases. This is why we used a High Resolution Melting (HRM) assay to monitor the trend of asymptomatic malaria in a malaria endemic area of Iran which is under elimination program.

Methods:

The peripheral blood was sampled from 271 clinically approved non-febrile individuals from a malaria endemic zone of southeastern Iran for asymptomatic malaria prevalence detection by microscopy, Rapid Diagnostic Tests (RDTs) and HRM methods. The HRM assay was done based on the amplification of 18S SSU rRNA gene.

Results:

The HRM assay revealed infections from three individuals out of 271 (1.1% asymptomatic malaria prevalence) from the participants, two Iranian natives with Plasmodium vivax infection and one Pakistani immigrant with P. falciparum infection. Neither microscopy nor RDTs detected Plasmodium spp infections from the 271 non-febrile individuals. The nucleotide sequencing analysis of the positive controls used in this study showed a close homology with the reference gene bank sequences of P. falciparum 3D7 (CPO16995.1) and P. vivax Sal-1(UO3079.1).

Conclusion:

This study revealed a low frequency of asymptomatic malaria trend within malaria endemic areas of southeastern Iran which are under intense elimination program and also the ability of HRM assay in detecting low Plasmodium spp parasitemia beyond the limits of microscopy and RDTs.

An unlabelled probe-based real time PCR and modified semi-nested PCR as molecular tools for analysis of chloroquine resistant Plasmodium vivax isolates from Afghanistan

Background

Plasmodium vivax resistance to chloroquine (CQ) has been reported from many endemic regions in the world. Plasmodium vivax is responsible for 95% of malaria cases in Afghanistan and CQ is the first-line treatment given for vivax malaria. The pvmdr-1 and pvcrt-o (K10 insertion) genes are possible markers for CQ-resistance in P. vivax isolates. There have been no studies done on the presence or absence of molecular markers for CQ-resistance P. vivax in Afghanistan. The present work aimed to evaluate the frequency of mutations in the pvmdr-1 and K10 insertion in the pvcrt-o genes of P. vivax.

Methods

Plasmodium vivax isolates were collected from Laghman, Baghlan and Khost provinces. For investigation of polymorphisms of desired regions in pvmdr-1 and pvcrt-o genes, sequencing was applied on the PCR products. A new asymmetric qPCR and melting analysis assay based on unlabelled probe developed for scanning of K10 insertion in pvcrt-o gene.

Results

The analysis of sequencing data of the pvmdr-1 gene showed wild type Y976 and K997 and mutant M958 and L1076 in 33 isolates from three provinces. Of the 36 samples evaluated for K10 insertion in pvcrt-o, 2/18(11%), 0/10(0%) and 0/8(0%) isolates from Laghman, Baghlan and Khost province, respectively, possessed K10 insertion, confirmed by either sequencing and unlabelled probes.

Conclusion

Two samples with K10 insertion and 33 samples with pvmdr1 polymorphism, indicating on the possibility of CQ resistance in P. vivax populations in Afghanistan. Furthermore, unlabelled probes are simple and inexpensive alternative tools for screening of P. vivax mutations.

Effectiveness of plant-based repellents against different Anopheles species: a systematic review

Plant-based repellents have been applied for generations in traditional practice as a personal protection approach against different species of Anopheles. Knowledge of traditional repellent plants is a significant resource for the development of new natural products as an alternative to chemical repellents. Many studies have reported evidence of repellant activities of plant extracts or essential oils against malaria vectors worldwide. This systematic review aimed to assess the effectiveness of plant-based repellents against Anopheles mosquitoes. All eligible studies on the repellency effects of plants against Anopheles mosquitoes published up to July 2018 were systematically searched through PubMed/Medline, Scopus and Google scholar databases. Outcomes measures were percentage repellency and protection time. A total of 62 trials met the inclusion criteria. The highest repellency effect was identified from Ligusticum sinense extract, followed by citronella, pine, Dalbergia sissoo, peppermint and Rhizophora mucronata oils with complete protection time ranging from 9.1 to 11.5 h. Furthermore, essential oils from plants such as lavender, camphor, catnip, geranium, jasmine, broad-leaved eucalyptus, lemongrass, lemon-scented eucalyptus, amyris, narrow-leaved eucalyptus, carotin, cedarwood, chamomile, cinnamon oil, juniper, cajeput, soya bean, rosemary, niaouli, olive, tagetes, violet, sandalwood, litsea, galbanum, and Curcuma longa also showed good repellency with 8 h complete repellency against different species of Anopheles. Essential oils and extracts of some plants could be formulated for the development of eco-friendly repellents against Anopheles species. Plant oils may serve as suitable alternatives to synthetic repellents in the future as they are relatively safe, inexpensive, and are readily available in many parts of the world.

Induction of Immune Responses by DNA Vaccines Formulated with Dendrimer and Poly (Methyl Methacrylate) (PMMA) Nano-Adjuvants in BALB/c Mice Infected with Leishmania major

BACKGROUND:

Leishmaniasis is a parasitic disease induced by a protozoan from the genus Leishmania. No effective vaccine has yet been developed against the disease.

AIM:

In this work, two nano-vaccines, TSA recombinant plasmid and dendrimer and poly (methyl methacrylate) (PMMA) nanoparticles (as adjuvants), were designed and tested for their immunogenicity in BALB/c mice.

METHODS:

After the plasmid construction and preparation of adjuvants, three intramuscular injections of the nano-vaccines (100 µg) and the recombinant TSA protein (20 µg) were subcutaneously performed. Eventually, the challenged animals were infected with the parasites (1*10⁶ promastigotes). After the last injections of the nano-vaccines, the responses of their antibody subclasses and cytokines were assessed via ELISA method before and after the challenge.

RESULTS:

This study revealed that the new nano-vaccines were strong and effective in inducing specific antibody and cellular responses and reducing the parasite burden in the spleen compared to the control groups of Leishmania major-infected BALB/c mice.

CONCLUSION:

Based on the results, we can suggest that the formulated vaccines are suitable candidates for further studies in the field of leishmaniasis control.

Molecular detection of Leishmania spp. isolated from cutaneous lesions of patients referred to Herat regional hospital, Afghanistan

Cutaneous leishmaniasis is one of the main public health problems in Afghanistan, particularly in Herat. To identify Leishmania spp., molecular techniques were applied to samples from 64 cutaneous leishmaniasis patients referred to Herat regional hospital during 2013. Polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis of the ribosomal RNA gene internal transcribed spacer-1 (ITS1) was used. Most of the patients demonstrated dry type single lesions on the head. The results of direct microscopy detection using Giemsastained skin scrapings were compared with that of ITS PCR-RFLP for the diagnosis of cutaneous leishmaniasis. Light microscopy examination showed 37/64 positive cases (58%). PCR revealed 50 positive cases (78%), from which ITS PCR-RFLP identified 48 cases (96%) as L. tropica and 2 cases (4%) as L. major. Cutaneous leishmaniasis in Herat appears to be endemic and of the clinically dry type, caused mainly by L. tropica and occasionally by L. major.